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clodius aggregate: NameError: global name '_bigwig' is not defined #28
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I have the same issue. I even tried to use the docker in case it was some OS- or python-related issue, but I get the same error. Any ideas? |
It worked for me when running it in the higlass container (which has it installed). |
Thanks for the suggestion, but I got the same error. Perhaps we are using different versions of higlass. |
Maybe try pulling v0.2.63, which is what I'm using. |
That worked, thanks! Still, I hope they address this issue, as it seems it's being carried over to recent versions of Higlass as well... |
Btw, there's no need to aggregate bigwigs anymore. HiGlass can ingest them natively now ( |
That's great news! Very nice feature, thanks! |
Hi, The way I generate the bigwig file is the following: Do you have any idea on how I can solve the shift problem? Thanks |
There's a chromosome ordering bug at the moment related to non-primary scaffolds (random and Un contigs). If that's the problem, a workaround for now is to omit the non-primary scaffolds from your bigwig. The second option is to export bedGraph and use clodius. @pkerpedjiev Looks like clodius's bigwig option was removed in a655ff6 but the command wasn't deprecated. |
On ubuntu xenial with a fresh python 2.7.12 install, I get the following:
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